C. Millino | Università degli Studi di Padova (original) (raw)

Papers by C. Millino

Frontiers in Molecular Neuroscience

Octopus vulgaris is a cephalopod mollusk and an active marine predator that has been at the cente... more Octopus vulgaris is a cephalopod mollusk and an active marine predator that has been at the center of a number of studies focused on the understanding of neural and biological plasticity. Studies on the machinery involved in e.g., learning and memory, regeneration, and neuromodulation are required to shed light on the conserved and/or unique mechanisms that these animals have evolved. Analysis of gene expression is one of the most essential means to expand our understanding of biological machinery, and the selection of an appropriate set of reference genes is the prerequisite for the quantitative real-time polymerase chain reaction (qRT-PCR). Here we selected 77 candidate reference genes (RGs) from a pool of stable and relatively high-expressed transcripts identified from the full-length transcriptome of O. vulgaris, and we evaluated their expression stabilities in different tissues through geNorm, NormFinder, Bestkeeper, Delta-CT method, and RefFinder. Although various algorithms p...

Results of DNA microarray data analysis using iChip. The main output of iChip is a bed file forma... more Results of DNA microarray data analysis using iChip. The main output of iChip is a bed file format that we modified to include the reference gene for the enriched region and the reference probe enrichment score (the probe with the largest enrichment value in the region). More specifically, the fields are the following: chromosome (chr), genomic start and end position of the enriched region (gstart and gend respectively), the gene name associated to the probe with the largest enrichment value (gene), the enrichment value expressed as moderated t-statistics using eBayes function (limma-t), the row number of gstart and gend in the position matrix (rstart and rend respectively), the genomic position where the probe has the largest enrichment value (peakpos), the mean posterior probability of the probes in the enriched region (meanpp), the maximum posterior probability of the probes in the enriched region (maxpp) and the number of probes in the enriched region (nprobe). (XLS 242 kb)

Summary of the clinical characteristics of the RMS patients analyzed (PDF 36 kb)

Summary of features of RMS cell lines (PDF 4 kb)

International Journal of Environmental Research and Public Health, 2014

Silica (SiO 2) nanoparticles (NPs) have found extensive applications in industrial manufacturing,... more Silica (SiO 2) nanoparticles (NPs) have found extensive applications in industrial manufacturing, biomedical and biotechnological fields. Therefore, the increasing exposure to such ultrafine particles requires studies to characterize their potential cytotoxic effects in order to provide exhaustive information to assess the impact of nanomaterials on human health. The understanding of the biological processes involved in the development and maintenance of a variety of pathologies is improved by genome-wide approaches, and in this context, gene set analysis has emerged as a fundamental tool for the interpretation of the results. In this work we show how the use of a combination of gene-by-gene and gene set analyses can enhance the interpretation of results of in vitro treatment of A549 cells with Ludox ® colloidal amorphous silica nanoparticles. OPEN ACCESS By gene-by-gene and gene set analyses, we evidenced a specific cell response in relation to NPs size and elapsed time after treatment, with the smaller NPs (SM30) having higher impact on inflammatory and apoptosis processes than the bigger ones. Apoptotic process appeared to be activated by the up-regulation of the initiator genes TNFa and IL1b and by ATM. Moreover, our analyses evidenced that cell treatment with Ludox  silica nanoparticles activated the matrix metalloproteinase genes MMP1, MMP10 and MMP9. The information derived from this study can be informative about the cytotoxicity of Ludox ® and other similar colloidal amorphous silica NPs prepared by solution processes.

OMICS: A Journal of Integrative Biology, 2009

The large dimension of microarray data and the complex dependence structure among genes make data... more The large dimension of microarray data and the complex dependence structure among genes make data analysis extremely challenging. In the last decade several statistical techniques have been proposed to tackle genome-wide expression data; however, clinical and molecular data associated to pathologies have often been considered as separate dimensions of the same phenomenon, especially when clinical variables lie on a multidimensional space. A better comprehension of the relationships between clinical and molecular data can be obtained if both data types are combined and integrated. In this work we adopt a multidimensional correlation strategy together with linear and nonlinear principal component, to integrate genetic and clinical information obtained from two sets of dystrophic patients. With this approach we decompose different aspects of clinical manifestations and correlate these features with the correspondent patterns of differential gene expression.

Journal of Biological Chemistry, 1998

The cardiac troponin I gene is one of the few sarcomeric protein genes exclusively expressed in c... more The cardiac troponin I gene is one of the few sarcomeric protein genes exclusively expressed in cardiac muscle. We show here that this specificity is controlled by a proximal promoter (؊230/؉16) in transfected cardiac cells in culture, in the adult hearts, and in transgenic animals. Functional analysis indicates that MEF2/Oct-1, Sp1, and GATA regulatory elements are required for optimal gene activation because selective mutations produce weak or inactive promoters. MEF2 and Oct-1 transcription factors bind to the same A/T-rich element. A mutation that blocks this binding markedly reduces gene activation in vivo and in vitro, and overexpression of MEF2A, MEF2C, and MEF2D in noncardiac cells transactivates the cardiac troponin I promoter. Disruption of these elements inactivates the cardiac troponin I promoter in cultured cardiac cells but has a less important role in transfected adult heart. Moreover, nuclear extracts from an almost pure population of adult cardiac cells contain much lower levels of GATA binding activity compared with fetal cardiac cells. These findings point to a differential role of GATA factors in the maintenance of gene expression in the adult heart as compared with the activation of cardiac genes in fetal cardiomyocytes. Overexpression of GATA family members transactivates the cardiac troponin I promoter, and GATA-5 and GATA-6 are stronger transactivators than GATA-4, a property apparently unique to the cardiac troponin I promoter. Transgenic mice carrying the ؊230/؉126 base pair promoter express ␤-galactosidase reporter gene in the heart both at early stages of cardiogenesis and in the adult animals. These results indicate that the ability of the cardiac troponin I proximal promoter to target expression of a downstream gene in the heart is also maintained when the transgene is integrated into the genome.

Developments in Cardiovascular Medicine, 1999

Different types of regulatory genes are involved in cardiac muscle development and cardiac gene r... more Different types of regulatory genes are involved in cardiac muscle development and cardiac gene regulation, including ubiquitous factors, such as SRF, SP1 and TEF-1, and genes coding for specific transcription factors: MADS-box transcription factor genes, such as the MEF2 genes which are also involved in the specification of skeletal and smooth muscle, homeobox genes, such as Nkx2.5, zinc-finger genes of the GATA family, such as GATA 4–6, and bHLH genes, such as dHAND and eHAND [1,2]. Gene regulation seems to require combinatorial interactions between cardiac-specific and ubiquitous factors: for example a physical interaction between Nkx2.5 and SRF is involved in the activation of the cardiac a-actin gene [3]. The study of cardiac gene regulation is complicated by the specific pattern of transcription of each gene, both with respect to temporal specificity during development and spatial specificity in the various heart chambers, presumably reflecting a modular regulation via multiple cis-acting elements [4]. Multiple approaches, including promoter analyses in cultured cells, in adult heart and in transgenic mice, are required to dissect the activity in time and space of cardiac regulatory genes and their combinatorial interactions.

BMC cancer, Jan 14, 2016

Rhabdomyosarcoma (RMS), which can be classified as embryonal RMS (ERMS) and alveolar RMS (ARMS), ... more Rhabdomyosarcoma (RMS), which can be classified as embryonal RMS (ERMS) and alveolar RMS (ARMS), represents the most frequent soft tissue sarcoma in the pediatric population; the latter shows greater aggressiveness and metastatic potential with respect to the former. Epigenetic alterations in cancer include DNA methylation changes and histone modifications that influence overall gene expression patterns. Different tumor subtypes are characterized by distinct methylation signatures that could facilitate early disease detection and greater prognostic accuracy. A genome-wide approach was used to examine methylation patterns associated with different prognoses, and DNA methylome analysis was carried out using the Agilent Human DNA Methylation platform. The results were validated using bisulfite sequencing and 5-aza-2'deoxycytidine treatment in RMS cell lines. Some in vitro functional studies were also performed to explore the involvement of a target gene in RMS tumor cells. In accor...

Journal of Biological Chemistry, 2014

Background: Mutations in SURF1, a human gene important for the assembly of cytochrome-c-oxidase (... more Background: Mutations in SURF1, a human gene important for the assembly of cytochrome-c-oxidase (COX) causes Leigh Syndrome, a mitochondrial encephalopathy. Results: Knockdown of Surf1 in Drosophila matches the biochemical features of the human disease. Conclusion: In Drosophila SURF1 is essential to maintain mitochondrial function and its silencing leads to COX deficiency. Significance: Drosophila offers new tools to investigate the pathogenic mechanism of Leigh Syndrome.

PLoS ONE, 2013

Background: Polar environments are characterized by extreme seasonal changes in day length, light... more Background: Polar environments are characterized by extreme seasonal changes in day length, light intensity and spectrum, the extent of sea ice during the winter, and food availability. A key species of the Southern Ocean ecosystem, the Antarctic krill (Euphausia superba) has evolved rhythmic physiological and behavioral mechanisms to adapt to daily and seasonal changes. The molecular organization of the clockwork underlying these biological rhythms is, nevertheless, still only partially understood. Methodology/Principal Findings: The genome sequence of the Antarctic krill is not yet available. A normalized cDNA library was produced and pyrosequenced in the attempt to identify large numbers of transcripts. All available E. superba sequences were then assembled to create the most complete existing oligonucleotide microarray platform with a total of 32,217 probes. Gene expression signatures of specimens collected in the Ross Sea at five different time points over a 24hour cycle were defined, and 1,308 genes differentially expressed were identified. Of the corresponding transcripts, 609 showed a significant sinusoidal expression pattern; about 40% of these exibithed a 24-hour periodicity while the other 60% was characterized by a shorter (about 12-hour) rhythm. We assigned the differentially expressed genes to functional categories and noticed that those concerning translation, proteolysis, energy and metabolic process, redox regulation, visual transduction and stress response, which are most likely related to daily environmental changes, were significantly enriched. Two transcripts of peroxiredoxin, thought to represent the ancestral timekeeping system that evolved about 2.5 billion years ago, were also identified as were two isoforms of the EsRh1 opsin and two novel arrestin1 sequences involved in the visual transduction cascade. Conclusions: Our work represents the first characterization of the krill diurnal transcriptome under natural conditions and provides a first insight into the genetic regulation of physiological changes, which occur around the clock during an Antarctic summer day.

BMC Medicine, 2009

Background: Spinal muscular atrophy (SMA) is a neurodegenerative disorder associated with mutatio... more Background: Spinal muscular atrophy (SMA) is a neurodegenerative disorder associated with mutations of the survival motor neuron gene SMN and is characterized by muscle weakness and atrophy caused by degeneration of spinal motor neurons. SMN has a role in neurons but its deficiency may have a direct effect on muscle tissue.

Gut, 2004

We verified whether conditioned media (CM) from pancreatic cancer cell lines (MIAPaCa2, CAPAN-1, ... more We verified whether conditioned media (CM) from pancreatic cancer cell lines (MIAPaCa2, CAPAN-1, PANC-1, BxPC3) alter glucose metabolism and gene expression profiles (microarray experiment with a platform of 5000 skeletal muscle cDNA) in mice myoblasts. Myoblasts were incubated with control or pancreatic cancer CM for 24 and 48 hours. Lactate significantly increased in CM compared with non-conditioned myoblasts. No variations in expression levels of the main genes involved in glycolysis were found in CM myoblasts. Propionyl coenzyme A carboxylase and isocitrate dehydrogenase 3 beta genes, which encode enzymes of the tricarboxylic acid cycle, were overexpressed, while IGFIIR and VAMP5 genes were underexpressed in CM myoblasts. PAFAH1B1 and BCL-2 genes (intracellular signal transduction) and the serine protease cathepsin G (proteolysis), were overexpressed in CM myoblasts. Tyrosine accumulation in CM myoblasts suggested that proteolysis overcomes protein synthesis. Sorcin, actin alpha...

Arteriosclerosis, thrombosis, and vascular biology, 1999

During the "response-to-injury" process after a mechanical insult to the porcine corona... more During the "response-to-injury" process after a mechanical insult to the porcine coronary arteries, the adventitial cells acquire the structural characteristics of myofibroblasts before being incorporated into smooth muscle (SM) layer. We assessed whether the SM-specific SM22 protein can be used as a tracer of adventitial cell-myofibroblast differentiation in the mild balloon injury of rabbit carotid artery. To achieve this goal, we used 2 monoclonal anti-SM22 antibodies (E-11 and 1-B8) and a molecular probe for the SM22alpha mRNA isoform in immunocytochemical and in situ hybridization experiments. The differentiation profile and the migratory and proliferative ability of activated adventitial cells were evaluated by a panel of antibodies to some SM and nonmuscle antigens and pulse- and end-labeling with bromo-deoxyuridine, respectively. In adventitial cells, SM22 antigenicity and SM22alpha mRNA were detectable at days 2 and 4 and, to a lesser extent, at days 7 and 21 afte...

Journal of Molecular Biology, 2003

We have characterized a novel unconventional myosin heavy chain, named MYO18B, that appears to be... more We have characterized a novel unconventional myosin heavy chain, named MYO18B, that appears to be expressed mainly in human cardiac and skeletal muscles and, at lower levels, in testis. MYO18B transcript is detected in all types of striated muscles but at much lower levels compared to class II sarcomeric myosins, and it is up regulated after in vitro differentiation of myoblasts into myotubes. Phylogenetic analysis shows that this myosin belongs to the recently identified class XVIII, however, unlike the other member of this class, it seems to be unique to Vertebrate since it contains two large amino acid domains of unknown function at the N and C-termini. Immunolocalization of MYO18B protein in skeletal muscle cells shows that this myosin heavy chain is located in the cytoplasm of undifferentiated myoblasts. After in vitro differentiation into myotubes, a fraction of this protein is accumulated in a subset of myonuclei. This nuclear localization was confirmed by immunofluorescence experiments on primary cardiomyocytes and adult muscle sections. In the cytoplasm MYO18B shows a punctate staining, both in cardiac and skeletal fibers. In some cases, cardiomyocytes show a partial sarcomeric pattern of MYO18B alternating that of alpha-actinin-2. In skeletal muscle the cytoplasmic MYO18B results much more evident in the fast type fibers.

Developmental Dynamics, 2000

Previous studies have demonstrated that the primordial pulmonary veins originate as an outgrowth ... more Previous studies have demonstrated that the primordial pulmonary veins originate as an outgrowth of the atrial cells and anastomosis with the pulmonary venous plexus. As a consequence of this embryologic origin the tunica media of these vessels is composed of cardiac cells that express atrial specific markers (Lyons et al. [1990] J Cell Biol 111:2427-2436; Jones et al. [1994] Dev Dyn 200:117-128). We used transgenic mice for the cardiac troponin I (cTNI) gene and smooth muscle (SM) myosin heavy chain as differentiation markers, to analyze how cardiac and SM cells contribute to the formation and structural remodeling of the pulmonary veins during development. We show here that the tunica media of the adult mouse pulmonary veins contains an outer layer of cardiac cells and an intermediate SM cell compartment lining down on the inner endothelium. This structural organization is well expressed in the intrapulmonary veins from the beginning of vasculogenesis, with cardiac cells accumulating over preexisting roots of endothelial and SM cells and extending to the third bifurcation of the pulmonary branches without reaching the more distal tips of the vessels. On the other hand, SM cells, which are widely distributed in the intrapulmonary veins from the embryonic stage E16, accumulate also in the extrapulmonary branches and reach the posterior wall of the left atrium, including the orifices of the pulmonary veins. This event takes place around birth when the pulmonary blood flow starts to function properly. A model for the development of the pulmonary veins is presented, based upon our analysis. Dev Dyn 2000;218:414 -425.